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Adding more examples to the gallery #80

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cb6103a
add notebooks
kolibril13 Aug 7, 2024
dbc2498
add torso notebook
kolibril13 Aug 14, 2024
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228 changes: 228 additions & 0 deletions examples/01_download_all_data.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Fetching contents from https://api.github.com/repos/niivue/niivue/contents/demos/images?ref=main...\n",
"Downloading AIL.nii.gz...\n",
"Downloading BrainMesh_ICBM152.lh.curv...\n",
"Downloading BrainMesh_ICBM152.lh.motor.mz3...\n",
"Downloading BrainMesh_ICBM152.lh.mz3...\n",
"Downloading CIT168.mz3...\n",
"Downloading ColumnMajorOrder.gii...\n",
"Downloading Conte69.L.inflated.32k_fs_LR.surf.gii...\n",
"Downloading Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii...\n",
"Downloading Conte69.R.inflated.32k_fs_LR.surf.gii...\n",
"Downloading DoG.png...\n",
"Downloading FA.nii.gz...\n",
"Downloading FLAIR.nii.gz...\n",
"Downloading FLAIR.nrrd...\n",
"Downloading FreeSurferControlPoints.json...\n",
"Downloading Human.colin.Cerebral.R.VERY_INFLATED.71723.surf.gii...\n",
"Downloading Human.colin.R.FUNCTIONAL.71723.func.gii...\n",
"Downloading MNI152_2009_template.nii.gz...\n",
"Downloading MolView-sticks-color_38.x3d...\n",
"Downloading TR_S_R.tt.gz...\n",
"Downloading V1.nii.gz...\n",
"Downloading aal.json...\n",
"Downloading aal.mz3...\n",
"Downloading aal.nii.gz...\n",
"Entering directory afni...\n",
"Fetching contents from https://api.github.com/repos/niivue/niivue/contents/demos/images/afni?ref=main...\n",
"Downloading DT_FA+orig.BRIK.gz...\n",
"Downloading DT_FA+orig.HEAD...\n",
"Downloading DT_V1+orig.BRIK.gz...\n",
"Downloading DT_V1+orig.HEAD...\n",
"Downloading anat_final.FT+tlrc.BRIK...\n",
"Downloading anat_final.FT+tlrc.HEAD...\n",
"Downloading avg152T1_RL_nifti.nii.gz...\n",
"Downloading boggle.lh.annot...\n",
"Downloading cactus.nii.gz...\n",
"Downloading colby.trk...\n",
"Downloading colby.trx...\n",
"Downloading complex.nii.gz...\n",
"Downloading connectome.jcon...\n",
"Downloading connectome2.jcon...\n",
"Downloading cope1.nii.gz...\n",
"Downloading ct_perfusion.nii.gz...\n",
"Downloading dpsv.trx...\n",
"Downloading draw.nii.gz...\n",
"Downloading dsistudio.fib.gz...\n",
"Downloading dsistudio.src.gz...\n",
"Downloading enh.dcm...\n",
"Downloading example4d+orig.BRIK.gz...\n",
"Downloading example4d+orig.HEAD...\n",
"Entering directory fs...\n",
"Fetching contents from https://api.github.com/repos/niivue/niivue/contents/demos/images/fs?ref=main...\n",
"Downloading brainmask.mgz...\n",
"Downloading lh.pial...\n",
"Downloading lh.white...\n",
"Downloading rh.pial...\n",
"Downloading rh.white...\n",
"Downloading wm.mgz...\n",
"Downloading fs_LR.32k.L.inflated.surf.gii...\n",
"Downloading fs_LR.32k.LR.curvature.dscalar.nii...\n",
"Downloading fslmean.nii.gz...\n",
"Downloading fslt.nii.gz...\n",
"Downloading hippo.nii.gz...\n",
"Downloading hippolr.nii.gz...\n",
"Downloading inia19-NeuroMaps.json...\n",
"Downloading inia19-NeuroMaps.nii.gz...\n",
"Downloading inia19-t1-brain.nii.gz...\n",
"Downloading labels256.nii.gz...\n",
"Downloading lesion.nii.gz...\n",
"Downloading lh.Yeo2011.gii...\n",
"Downloading lh.Yeo2011.mgz...\n",
"Downloading lh.curv...\n",
"Downloading lh.pial...\n",
"Downloading low_res.nii.gz...\n",
"Downloading mean_func.nii.gz...\n",
"Downloading minimal.nii.gz...\n",
"Downloading mni152.SLF1_R.tsf...\n",
"Downloading mni152.nii.gz...\n",
"Downloading mni152_pveseg.nii.gz...\n",
"Downloading mni_format.obj.gz...\n",
"Downloading motor_4t95mesh.rh.mz3...\n",
"Entering directory mz3...\n",
"Fetching contents from https://api.github.com/repos/niivue/niivue/contents/demos/images/mz3?ref=main...\n",
"Downloading 11ScalarMesh.mz3...\n",
"Downloading 16DoubleOverlay_5124x2.mz3...\n",
"Downloading 3Mesh.mz3...\n",
"Downloading README.md...\n",
"Downloading cortex_5124.mz3...\n",
"Downloading narps-4735_50GV-hypo1_unthresh.nii.gz...\n",
"Downloading narps-4965_9U7M-hypo1_unthresh.nii.gz...\n",
"Downloading niivue-drawing.nvd...\n",
"Downloading niivue-with-clip-plane.nvd...\n",
"Downloading niivue.basic.nvd...\n",
"Downloading niivue.drawing.nvd...\n",
"Downloading niivue.mesh.nvd...\n",
"Downloading niivue1-no-hippo.nvd...\n",
"Downloading niivue1.nvd...\n",
"Downloading otsu.nii.gz...\n",
"Downloading pcasl.nii.gz...\n",
"Downloading pcasl.png...\n",
"Downloading pval.LH.nii.gz...\n",
"Downloading scaled+tlrc.BRIK.gz...\n",
"Downloading scaled+tlrc.HEAD...\n",
"Downloading shear.nii.gz...\n",
"Downloading simplify_brain.obj...\n",
"Downloading spmMotor.nii.gz...\n",
"Downloading stats.FT+tlrc.BRIK...\n",
"Downloading stats.FT+tlrc.HEAD...\n",
"Downloading stats.nv_demo_mskd.nii.gz...\n",
"Downloading sub-01_ses-01_dwi_desc-b0_dwi.nii.gz...\n",
"Downloading sub-01_ses-01_dwi_space-RASMM_model-probCSD_algo-AFQ_tractography.trx...\n",
"Downloading sub-test02_left_hemisphere.srf.gz...\n",
"Downloading sub-test02_left_hemisphere_4_curvature_maps.smp.gz...\n",
"Downloading template.mif.gz...\n",
"Downloading torso.nii.gz...\n",
"Downloading torsoLabel.nii.gz...\n",
"Downloading tract.FAT_R.vtk...\n",
"Downloading tract.IFOF_R.trk...\n",
"Downloading tract.SLF1_R.tck...\n",
"Entering directory trix...\n",
"Fetching contents from https://api.github.com/repos/niivue/niivue/contents/demos/images/trix?ref=main...\n",
"Downloading fa.mif...\n",
"Downloading mask_1bit.mif...\n",
"Downloading tensors.mif...\n",
"Downloading v1.mif...\n",
"Downloading tstat1.nii.gz...\n",
"Downloading vr_base_min_outlier+orig.BRIK...\n",
"Downloading vr_base_min_outlier+orig.HEAD...\n",
"Downloading wm.mgz...\n",
"Downloading xd.mz3...\n",
"Downloading yd.mz3...\n",
"Downloading yeh2022.trx...\n",
"Downloading zd.mz3...\n",
"All files and subdirectories have been downloaded to images.\n"
]
}
],
"source": [
"# Import necessary libraries\n",
"import os\n",
"import requests\n",
"import json\n",
"\n",
"# GitHub API URL for the base folder\n",
"BASE_API_URL = \"https://api.github.com/repos/niivue/niivue/contents\"\n",
"FOLDER_PATH = \"demos/images\"\n",
"REF = \"main\"\n",
"\n",
"# Folder where files will be saved\n",
"DEST_FOLDER = \"images\"\n",
"\n",
"# Function to fetch and download files recursively\n",
"def fetch_and_download(api_url, dest_folder):\n",
" print(f\"Fetching contents from {api_url}...\")\n",
" os.makedirs(dest_folder, exist_ok=True)\n",
" response = requests.get(api_url)\n",
" if response.status_code != 200:\n",
" print(f\"Failed to fetch {api_url}: {response.status_code}\")\n",
" return\n",
" \n",
" file_list = response.json()\n",
" for item in file_list:\n",
" item_type = item['type']\n",
" download_url = item.get('download_url', '') if item_type == 'file' else ''\n",
" name = item['name']\n",
" path = item['path']\n",
" html_url = item['html_url']\n",
"\n",
" if item_type == 'file':\n",
" print(f\"Downloading {name}...\")\n",
" file_response = requests.get(download_url)\n",
" if file_response.status_code == 200:\n",
" with open(os.path.join(dest_folder, name), 'wb') as f:\n",
" f.write(file_response.content)\n",
" else:\n",
" print(f\"Failed to download {name}: {file_response.status_code}\")\n",
" elif item_type == 'dir':\n",
" print(f\"Entering directory {name}...\")\n",
" subfolder = os.path.join(dest_folder, name)\n",
" sub_api_url = f\"{BASE_API_URL}/{path}?ref={REF}\"\n",
" fetch_and_download(sub_api_url, subfolder)\n",
"\n",
"# Start the recursive downloading\n",
"fetch_and_download(f\"{BASE_API_URL}/{FOLDER_PATH}?ref={REF}\", DEST_FOLDER)\n",
"\n",
"print(f\"All files and subdirectories have been downloaded to {DEST_FOLDER}.\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": ".venv",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
92 changes: 47 additions & 45 deletions examples/additive_voxels.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,35 +2,39 @@
"cells": [
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"!mkdir -p ../images/\n",
"!wget https://github.com/niivue/niivue/raw/main/demos/images/narps-4735_50GV-hypo1_unthresh.nii.gz -P ../images/\n",
"!wget https://github.com/niivue/niivue/raw/main/demos/images/narps-4965_9U7M-hypo1_unthresh.nii.gz -P ../images/\n",
"!wget https://github.com/niivue/niivue/raw/main/demos/images/mni152.nii.gz -P ../images/"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "8e77b0fab1204e5191dbca06414c09a4",
"version_major": 2,
"version_minor": 1
},
"text/plain": [
"NiiVue(height=300)"
]
},
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from ipyniivue import NiiVue, SliceType\n",
"# based on https://niivue.github.io/niivue/features/additive.voxels.html\n",
"\n",
"volumes = [\n",
" { \"path\": \"../images/mni152.nii.gz\" },\n",
" { \"path\": \"images/mni152.nii.gz\" },\n",
" {\n",
" \"path\": \"../images/narps-4965_9U7M-hypo1_unthresh.nii.gz\",\n",
" \"path\": \"images/narps-4965_9U7M-hypo1_unthresh.nii.gz\",\n",
" \"colormap\": \"red\",\n",
" \"cal_min\": 2,\n",
" \"cal_max\": 4,\n",
" },\n",
" {\n",
" \"path\": \"../images/narps-4735_50GV-hypo1_unthresh.nii.gz\",\n",
" \"path\": \"images/narps-4735_50GV-hypo1_unthresh.nii.gz\",\n",
" \"colormap\": \"green\",\n",
" \"cal_min\": 2,\n",
" \"cal_max\": 4,\n",
Expand All @@ -47,9 +51,25 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "cb5b42ba9d774dd69a613e644326eb2f",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"HBox(children=(FloatSlider(value=0.2, max=0.4, min=0.1, step=0.01), FloatSlider(value=0.2, max=0.4, min=0.1, s…"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import ipywidgets\n",
"\n",
Expand All @@ -60,34 +80,16 @@
"ipywidgets.link((sgreen, \"value\"), (nv.volumes[2], \"cal_min\"))\n",
"ipywidgets.HBox([sred, sgreen])"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
},
],
"metadata": {},
"nbformat": 4,
"nbformat_minor": 4
}
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